The Environmental Protection Agency's final report on a five-year study finds hydraulic fracturing can in fact contaminate drinking water in some cases.

The EPA's presentation of the final assessment marks a significant change in the way the report was initially presented in 2015. Energy companies seized on that presentation because it said the EPA found no "widespread, systemic impact" on drinking water supplies.

The drilling method, also known as "fracking," involves pumping a mixture of water, minerals and chemicals into the ground at high pressure to fracture shale rock and release oil and natural gas. The technology, along with horizontal drilling, has underpinned a massive boom in U.S. oil and gas production.

The EPA found cases of effects on drinking water at each stage of the fracking water cycle, from acquisition to disposal.

The effects discussed in the report tended to happen near fracking wells. Cases ranged from mere temporary water quality changes to levels of contamination that made drinking wells unusable.

The EPA noted that "data gaps and uncertainties" limited the agency's ability to fully assess the risks of fracking to groundwater supplies.

"In places where we know activities in the hydraulic fracturing water cycle have occurred, data that could be used to characterize hydraulic fracturing-related chemicals in the environment before, during, and after hydraulic fracturing were scarce," the agency said in a news release.

"Because of these data gaps and uncertainties, as well as others described in the assessment, it was not possible to fully characterize the severity of impacts, nor was it possible to calculate or estimate the national frequency of impacts on drinking water resources from activities in the hydraulic fracturing water cycle."

The American Petroleum Institute, which represents energy companies, blasted the final report, saying there is ample research that demonstrates the oil and gas industry and regulatory programs protect water resources "at every step of the hydraulic fracturing process."

"It is beyond absurd for the administration to reverse course on its way out the door," API Upstream Director Erik Milito said in a statement, referring to the EPA's earlier presentation in 2015.

But the final report actually marks a return to the message on which the EPA had originally focused. An investigation by Marketplace and APM Reports suggested last minute changes downplayed the risk hydraulic fracturing presented to drinking water.

The EPA's initial press release and executive summary of the study released last year emphasized a key phrase: "hydraulic fracturing activities have not led to widespread, systemic impacts to drinking water resources." Energy industry groups and media organizations, including CNBC.com, have widely cited the finding in discussions of fracking's safety.

The phrase was added to a draft press release in May of 2015 prior to its public release in June, Marketplace and APM's investigation found. The EPA's messaging had earlier put more emphasis on vulnerabilities to water supplies and about two dozen cases in which fracking operations had affected water resources, according to drafts obtained by Marketplace and APM.

People familiar with the research told Marketplace and APM the choice to say there was no "widespread, systemic" impact on water supplies from fracking was "bizarre," "irresponsible" and "ambiguous."

The broad conclusion was simply not backed up by measurable data, according to Peter Thorne, chairman of the EPA's Science Advisory Board.